Traditional navigation services find the fastest route for a single driver. Though always using the fastest route seems desirable for every individual, selfish behavior can have undesirable effects such as higher energy consumption and avoidable congestion, even leading to higher overall and individual travel times. In contrast, strategic routing aims at optimizing the traffic for all agents regarding a global optimization goal. We introduce a framework to formalize real-world strategic routing scenarios as algorithmic problems and study one of them, which we call Single Alternative Path (SAP), in detail. There, we are given an original route between a single origin--destination pair. The goal is to suggest an alternative route to all agents that optimizes the overall travel time under the assumption that the agents distribute among both routes according to a psychological model, for which we introduce the concept of Pareto-conformity. We show that the SAP problem is NP-complete, even for such models. Nonetheless, assuming Pareto-conformity, we give multiple algorithms for different variants of SAP, using multi-criteria shortest path algorithms as subroutines. Moreover, we prove that several natural models are in fact Pareto-conform. The implementation of our algorithms serves as a proof of concept, showing that SAP can be solved in reasonable time even though the algorithms have exponential running time in the worst case.

A popular clustering algorithm for biological networks which was proposed by Hartuv and Shamir identifies nonoverlapping highly connected components. We extend the approach taken by this algorithm by introducing the combinatorial optimization problem Highly Connected Deletion, which asks for removing as few edges as possible from a graph such that the resulting graph consists of highly connected components. We show that Highly Connected Deletion is NP-hard and provide a fixed-parameter algorithm and a kernelization. We propose exact and heuristic solution strategies, based on polynomial-time data reduction rules and integer linear programming with column generation. The data reduction typically identifies 75 percent of the edges that are deleted for an optimal solution; the column generation method can then optimally solve protein interaction networks with up to 6,000 vertices and 13,500 edges within five hours. Additionally, we present a new heuristic that finds more clusters than the method by Hartuv and Shamir.

We consider the discrepancy problem of coloring n intervals with k colors such that at each point on the line, the maximal difference between the number of intervals of any two colors is minimal. Somewhat surprisingly, a coloring with maximal difference at most one always exists. Furthermore, we give an algorithm with running time O(n log n + kn log k) for its construction. This is in particular interesting because many known results for discrepancy problems are non-constructive. This problem naturally models a load balancing scenario, where $n$~tasks with given start- and endtimes have to be distributed among $k$~servers. Our results imply that this can be done ideally balanced. When generalizing to $d$-dimensional boxes (instead of intervals), a solution with difference at most one is not always possible. We show that for any d >= 2 and any k >= 2 it is NP-complete to decide if such a solution exists, which implies also NP-hardness of the respective minimization problem. In an online scenario, where intervals arrive over time and the color has to be decided upon arrival, the maximal difference in the size of color classes can become arbitrarily high for any online algorithm.

In the network querying problem, one is given a protein complex or pathway of species A and a protein-protein interaction network of species B; the goal is to identify subnetworks of B that are similar to the query in terms of sequence, topology, or both. Existing approaches mostly depend on knowledge of the interaction topology of the query in the network of species A; however, in practice, this topology is often not known. To address this problem, we develop a topology-free querying algorithm, which we call Torque. Given a query, represented as a set of proteins, Torque seeks a matching set of proteins that are sequence-similar to the query proteins and span a connected region of the network, while allowing both insertions and deletions. The algorithm uses alternatively dynamic programming and integer linear programming for the search task. We test Torque with queries from yeast, fly, and human, where we compare it to the QNet topology-based approach, and with queries from less studied species, where only topology-free algorithms apply. Torque detects many more matches than QNet, while giving results that are highly functionally coherent.

The fixed-parameter approach is an algorithm design technique for solving combinatorially hard (mostly NP-hard) problems. For some of these problems, it can lead to algorithms that are both efficient and yet at the same time guaranteed to find optimal solutions. Focusing on their application to solving NP-hard problems in practice, we survey three main techniques to develop fixed-parameter algorithms, namely: kernelization (data reduction with provable performance guarantee), depth-bounded search trees and a new technique called iterative compression. Our discussion is circumstantiated by several concrete case studies and provides pointers to various current challenges in the field.

UNLABELLED: Faspad is a user-friendly tool that detects candidates for linear signaling pathways in protein interaction networks based on an approach by Scott et al. (Journal of Computational Biology, 2006). Using recent algorithmic insights, it can solve the underlying NP-hard problem quite fast: for protein networks of typical size (several thousand nodes), pathway candidates of length up to 13 proteins can be found within seconds and with a 99.9% probability of optimality. Faspad graphically displays all candidates that are found; for evaluation and comparison purposes, an overlay of several candidates and the surrounding network context can also be shown. AVAILABILITY: Faspad is available as free software under the GPL license at http://theinf1.informatik.uni-jena.de/faspad/ and runs under Linux and Windows.

To cover the edges of a graph with a minimum number of cliques is an NP-complete problem with many applications. The state-of-the-art solving algorithm is a polynomial-time heuristic from the 1970's. We present an improvement of this heuristic. Our main contribution, however, is the development of efficient and effective polynomial-time data reduction rules that, combined with a search tree algorithm, allow for exact problem solutions in competitive time. This is confirmed by experiments with real-world and synthetic data. Moreover, we prove the fixed-parameter tractability of covering edges by cliques.